Analysis of recombination and gene distribution in the 2L1.0 region of wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.)

Both wheat and barley belong to tribe Triticeae and are closely related. High-density detailed comparison of physical and genetic linkage maps revealed that wheat genes are present in physically small gene-rich regions (GRRs). One of the largest GRRs is located around fraction length 1.0 of the long arm of wheat homoeologous group 2 chromosomes termed the "2L1.0 region." The main objective of this study was to analyze the structural and functional organization of the 2L1.0 region in barley in comparison to wheat. Using the 29 physically mapped RFLP markers for the region, wheat and barley consensus genetic linkage maps of the 2L1.0 region were generated by combining information from 18 wheat and 7 barley genetic linkage maps. Comparative analysis using these consensus maps and other available wheat and barley mapping resources identified 227 DNA markers and ESTs for the region. The region accounted for 58% of the genes and 68% of the arm's recombination in wheat. However, the corresponding region in barley accounted for about 42% of the genes and 81% of the recombination. The kb/cM ratio for the region was 122 in barley compared to 244 in wheat. Distribution of genes and recombination varied between the two species even though the gene order and density were similar.     

Saturation mapping of a gene-rich recombination hot spot region in wheat

Physical mapping of wheat chromosomes has revealed small chromosome segments of high gene density and frequent recombination interspersed with relatively large regions of low gene density and infrequent recombination. We constructed a detailed genetic and physical map of one highly recombinant region on the long arm of chromosome 5B. This distally located region accounts for 4% of the physical size of the long arm and at least 30% of the recombination along the entire chromosome. Multiple crossovers occurred within this region, and the degree of recombination is at least 11-fold greater than the genomic average. Characteristics of the region such as gene order and frequency of recombination appear to be conserved throughout the evolution of the Triticeae. The region is more prone to chromosome breakage by gametocidal gene action than gene-poor regions, and evidence for genomic instability was implied by loss of gene collinearity for six loci among the homeologous regions. These data suggest that a unique level of chromatin organization exists within gene-rich recombination hot spots. The many agronomically important genes in this region should be accessible by positional cloning.     

Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 5 of Wheat

The distribution of genes and recombination in the wheat genome was studied by comparing physical maps with the genetic linkage maps. The physical maps were generated by mapping 80 DNA and two phenotypic markers on an array of 65 deletion lines for homoeologous group 5 chromosomes. The genetic maps were constructed for chromosome 5B in wheat and 5D in Triticum tauschii. No marker mapped in the proximal 20% chromosome region surrounding the centromere. More than 60% of the long arm markers were present in three major clusters that physically encompassed <18% of the arm. Because 48% of the markers were cDNA clones and the distributions of the cDNA and genomic clones were similar, the marker distribution may represent the distribution of genes. The gene clusters were identified and allocated to very small chromosome regions because of a higher number of deletions in their surrounding regions. The recombination was suppressed in the centromeric regions and mainly occurred in the gene-rich regions. The bp/cM estimates varied from 118 kb for gene-rich regions to 22 Mb for gene-poor regions. The wheat genes present in these clusters are, therefore, amenable to molecular manipulations parallel to the plants with smaller genomes like rice.     

Distribution of genes and recombination on wheat homoeologous group <Emphasis Type="Italic">6</Emphasis> chromosomes: a synthesis of available information

Presence of genes in gene-rich regions on wheat chromosomes has been widely reported. However, there is a lack of information on the precise characterization of these regions with respect to the distribution of genes and recombination. We attempted to critically analyze the available data to characterize gene-rich regions and to study the distribution of genes and recombination on wheat homoeologous group 6 chromosomes which are a reservoir of several useful genes controlling traits of economic importance. Consensus physical and genetic linkage maps were constructed for homoeologous group 6 using physical and genetic mapping data. Five major gene-rich regions were identified on homoeologous group 6 chromosomes, with two on the short and three on long arm. More than 90% of marker or gene loci were present in these five gene-rich regions, which comprise about 30% of the total physical chromosomal length. The gene-rich regions were mainly present in the distal 60% regions of the chromosomes. About 61% of the total loci map in the most distal regions which span only about 4% of the physical length of the chromosome. A range of sub-microscopic regions within each gene-rich region were also identified. Comparisons of the consensus physical and genetic linkage maps revealed that recombination occurred mainly in the gene-rich regions. Seventy percent of the total recombination occurred in the two most distally located regions that span only 4% of the physical length of the chromosomes. The relationship of recombination to the gene-rich region is not linear with distance from the centromere, especially on the long arm. The kb/cM estimates for group 6 chromosomes ranged from 146 kb in the gene-rich to about 10 Mb in the gene-poor region. The information obtained here is vital in understanding wheat genome structure and organization, which may lead in developing better strategies for positional cloning in wheat and related cereals.This revised version was pubished online in April 2005 with corrections to the page numbering.     

Gene-containing regions of wheat and the other grass genomes

Deletion line-based high-density physical maps revealed that the wheat (Triticum aestivum) genome is partitioned into gene-rich and -poor compartments. Available deletion lines have bracketed the gene-containing regions to about 10% of the genome. Emerging sequence data suggest that these may further be partitioned into "mini" gene-rich and gene-poor regions. An average of about 10% of each gene-rich region seem to contain genes. Sequence analyses in various species suggest that uneven distribution of genes may be a characteristic of all grasses and perhaps all higher organisms. Comparison of the physical maps with genetic linkage maps showed that recombination in wheat and barley (Hordeum vulgare) is confined to the gene-containing regions. Number of genes, gene density, and the extent of recombination vary greatly among the gene-rich regions. The gene order, relative region size, and recombination are highly conserved within the tribe Triticeae and moderately conserved within the family. Gene-poor regions are composed of retrotransposon-like non-transcribing repeats and pseudogenes. Direct comparisons of orthologous regions indicated that gene density in wheat is about one-half compared with rice (Oryza sativa). Genome size difference between wheat and rice is, therefore, mainly because of amplification of the gene-poor regions. Presence of species-, genera-, and family-specific repeats reveal a repeated invasion of the genomes by different retrotransposons over time. Preferential transposition to adjacent locations and presence of vital genes flanking a gene-rich region may have restricted retrotransposon amplification to gene-poor regions, resulting into tandem blocks of non-transcribing repeats. Insertional inactivation by adjoining retro-elements and selection seem to have played a major role in stabilizing genomes.     

Structural and functional organization of the '1S0.8 gene-rich region' in the Triticeae

Wheat genes are present in physically small, gene-rich regions, interspersed by gene-poor blocks of retrotransposon-like repetitive sequences. One of the largest gene-rich regions is present around fraction length (FL) 0.8 of the short arm of wheat homoeologous group 1 chromosomes and is called `1S0.8 region'. The objective of this study was to reveal the structural and functional organization of the `1S0.8 region' in various Triticeae and other Poaceae species. Consensus genetic linkage maps of the `1S0.8 region' were constructed for wheat, barley, and rye by combining mapping information from 16, 11, and 12 genetic linkage maps, respectively. The consensus genetic linkage maps were compared with each other and with a consensus physical map of wheat homoeologous group 1. Comparative analyses localized 75 agronomically important genes to the `1S0.8 region'. This high-resolution comparison revealed exceptions to the rule of conserved gene synteny, established using low-resolution marker comparisons. Small rearrangements such as duplications, deletions, and inversions were observed among species. Proportion of chromosomal recombination occurring in the `1S0.8 region' was very similar among species. Within the gene-rich region, the extent of recombination was highly variable but the pattern was similar among species. Relative recombination among markers was similar except for a few loci where drastic differences were observed among species. Chromosomal rearrangements did not always change the extent of recombination for the region. Differences in gene order and relative recombination were the least between wheat and barley, and were the highest between wheat and oat.     

Genomic mapping of defense response genes in wheat

 Defense response (DR) genes are a broad class involved in plant defense. In this study we mapped 36 probes representing seven classes of defense response genes. This collection of probes represents genes involved in the hypersensitive response (HR), pathogenesis-related (PR) genes, genes for the flavonoid metabolic pathway, genes encoding proline/glycine-rich proteins, ion channel regulators, lipoxygenase, lectin, and others. Using nullisomic-tetrasomic lines of ‘Chinese Spring’, we were able to assign at least 167 loci to the 21 chromosomes of wheat. Homoeologous group 7 chromosomes possessed the most DR loci followed by group 2. Sixty-two loci were placed on existing genetic linkage maps of wheat. Map locations indicated that the DR gene loci are not randomly distributed throughout the wheat genome, but rather are located in clusters and/or in distal gene-rich regions of the chromosomes. Knowledge of the chromosomal locations and genome organization of DR genes will be useful for candidate gene analysis of quantitative trait loci. Received: 12 June 1998 / Accepted: 24 July 1998     

Cytologically integrated physical restriction fragment length polymorphism maps for the barley genome based on translocation breakpoints

We have developed a new technique for the physical mapping of barley chromosomes using microdissected translocation chromosomes for PCR with sequence-tagged site primers derived from >300 genetically mapped RFLP probes. The positions of 240 translocation breakpoints were integrated as physical landmarks into linkage maps of the seven barley chromosomes. This strategy proved to be highly efficient in relating physical to genetic distances. A very heterogeneous distribution of recombination rates was found along individual chromosomes. Recombination is mainly confined to a few relatively small areas spaced by large segments in which recombination is severely suppressed. The regions of highest recombination frequency (相似文献   

Comprehensive molecular cytogenetic analysis of sorghum genome architecture: distribution of euchromatin, heterochromatin, genes and recombination in comparison to rice

Cytogenetic maps of sorghum chromosomes 3-7, 9, and 10 were constructed on the basis of the fluorescence in situ hybridization (FISH) of approximately 18-30 BAC probes mapped across each of these chromosomes. Distal regions of euchromatin and pericentromeric regions of heterochromatin were delimited for all 10 sorghum chromosomes and their DNA content quantified. Euchromatic DNA spans approximately 50% of the sorghum genome, ranging from approximately 60% of chromosome 1 (SBI-01) to approximately 33% of chromosome 7 (SBI-07). This portion of the sorghum genome is predicted to encode approximately 70% of the sorghum genes ( approximately 1 gene model/12.3 kbp), assuming that rice and sorghum encode a similar number of genes. Heterochromatin spans approximately 411 Mbp of the sorghum genome, a region characterized by a approximately 34-fold lower rate of recombination and approximately 3-fold lower gene density compared to euchromatic DNA. The sorghum and rice genomes exhibit a high degree of macrocolinearity; however, the sorghum genome is approximately 2-fold larger than the rice genome. The distal euchromatic regions of sorghum chromosomes 3-7 and 10 are approximately 1.8-fold larger overall and exhibit an approximately 1.5-fold lower average rate of recombination than the colinear regions of the homeologous rice chromosomes. By contrast, the pericentromeric heterochromatic regions of these chromosomes are on average approximately 3.6-fold larger in sorghum and recombination is suppressed approximately 15-fold compared to the colinear regions of rice chromosomes.     

Meiotic Recombination, Noncoding DNA and Genomic Organization in Caenorhabditis Elegans

The genetic map of each Caenorhabditis elegans chromosome has a central gene cluster (less pronounced on the X chromosome) that contains most of the mutationally defined genes. Many linkage group termini also have clusters, though involving fewer loci. We examine the factors shaping the genetic map by analyzing the rate of recombination and gene density across the genome using the positions of cloned genes and random cDNA clones from the physical map. Each chromosome has a central gene-dense region (more diffuse on the X) with discrete boundaries, flanked by gene-poor regions. Only autosomes have reduced rates of recombination in these gene-dense regions. Cluster boundaries appear discrete also by recombination rate, and the boundaries defined by recombination rate and gene density mostly, but not always, coincide. Terminal clusters have greater gene densities than the adjoining arm but similar recombination rates. Thus, unlike in other species, most exchange in C. elegans occurs in gene-poor regions. The recombination rate across each cluster is constant and similar; and cluster size and gene number per chromosome are independent of the physical size of chromosomes. We propose a model of how this genome organization arose.     

Recombination occurs uniformly within the bronze gene, a meiotic recombination hotspot in the maize genome.

The bronze (bz) gene is a recombinational hotspot in the maize genome: its level of meiotic recombination per unit of physical length is > 100-fold higher than the genome's average and is the highest of any plant gene analyzed to date. Here, we examine whether recombination is also unevenly distributed within the bz gene. In yeast genes, recombination (conversion) is polarized, being higher at the end of the gene where recombination is presumably initiated. We have analyzed products of meiotic recombination between heteroallelic pairs of bz mutations in both the presence and absence of heterologies and have sequenced the recombination junction in 130 such Bz intragenic recombinants. We have found that in the absence of heterologies, recombination is proportional to physical distance across the bz gene. The simplest interpretation for this lack of polarity is that recombination is initiated randomly within the gene. Insertion mutations affect the frequency and distribution of intragenic recombination events at bz, creating hotspots and coldspots. Single base pair heterologies also affect recombination, with fewer recombination events than expected by chance occurring in regions of the bz gene with a high density of heterologies. We also provide evidence that meiotic recombination in maize is conservative, that is, it does not introduce changes, and that meiotic conversion tracts are continuous and similar in size to those in yeast.     

Microsatellite-based deletion bin system for the establishment of genetic-physical map relationships in wheat (<Emphasis Type="Italic">Triticum aestivum</Emphasis> L.)

Because of polyploidy and large genome size, deletion stocks of bread wheat are an ideal material for physically allocating ESTs and genes to small chromosomal regions for targeted mapping. To enhance the utility of deletion stocks for chromosome bin mapping, we characterized a set of 84 deletion lines covering the 21 chromosomes of wheat using 725 microsatellites. We localized these microsatellite loci to 94 breakpoints in a homozygous state (88 distal deletions, 6 interstitial), and 5 in a heterozygous state representing 159 deletion bins. Chromosomes from homoeologous groups 2 and 5 were the best covered (126 and 125 microsatellites, respectively) while the coverage for group 4 was lower (80 microsatellites). We assigned at least one microsatellite in up to 92% of the bins (mean 4.97 SSR/bin). Only a few discrepancies concerning marker order were observed. The cytogenetic maps revealed small genetic distances over large physical regions around the centromeres and large genetic to physical map ratios close to the telomeres. As SSRs are the markers of choice for many genetic and breeding studies, the mapped microsatellite loci will be useful not only for deletion stock verifications but also for allocating associated QTLs to deletion bins where numerous ESTs that could be potential candidate genes are currently assigned.     

High-density mapping and comparative analysis of agronomically important traits on wheat chromosome 3A

Bread wheat chromosome 3A has been shown to contain genes/QTLs controlling grain yield and other agronomic traits. The objectives of this study were to generate high-density physical and genetic-linkage maps of wheat homoeologous group 3 chromosomes and reveal the physical locations of genes/QTLs controlling yield and its component traits, as well as agronomic traits, to obtain a precise estimate of recombination for the corresponding regions and to enrich the QTL-containing regions with markers. Physical mapping was accomplished by 179 DNA markers mostly representing expressed genes using 41 single-break deletion lines. Polymorphism survey of cultivars Cheyenne (CNN) and Wichita (WI), and a substitution line of CNN carrying chromosome 3A from WI [CNN(WI3A)], with 142 RFLP probes and 55 SSR markers revealed that the extent of polymorphism is different among various group 3 chromosomal regions as well as among the homoeologs. A genetic-linkage map for chromosome 3A was developed by mapping 17 QTLs for seven agronomic traits relative to 26 RFLP and 15 SSR chromosome 3A-specific markers on 95 single-chromosome recombinant inbred lines. Comparison of the physical maps with the 3A genetic-linkage map localized the QTLs to gene-containing regions and accounted for only about 36% of the chromosome. Two chromosomal regions containing 9 of the 17 QTLs encompassed less than 10% of chromosome 3A but accounted for almost all of the arm recombination. To identify rice chromosomal regions corresponding to the particular QTL-containing wheat regions, 650 physically mapped wheat group 3 sequences were compared with rice genomic sequences. At an E value of E < or = 10(-5), 82% of the wheat group 3 sequences identified rice homologs, of which 54% were on rice chromosome 1. The rice chromosome 1 region collinear with the two wheat regions that contained 9 QTLs was about 6.5 Mb.     

A comprehensive linkage map of the pig based on a wild pig - Large White intercross

A comprehensive linkage map, including 236 linked markers with a total sex-average map length of about 2300 cM, covering nearly all parts of the pig genome has been established. Linkage groups were assigned to all 18 autosomes, the X chromosome and the X/Y pseudoautosomal region. Several new gene assignments were made including the assignment of linkage group U1 (EAK-HPX) to chromosome 9. The linkage map includes 77 type I loci informative for comparative mapping and 72 in situ mapped markers physically anchoring the linkage groups on chromosomes. A highly significant heterogeneity in recombination rates between sexes was observed with a general tendency towards an excess of female recombination. The average ratio of female to male recombination was estimated at 1–4:1 but this parameter varied between chromosomes as well as between regions within chromosomes. An intriguing finding was that blood group loci were overrepresented at the distal ends of linkage groups.     

Locally Adaptive Inversions Modulate Genetic Variation at Different Geographic Scales in a Seaweed Fly

Across a species range, multiple sources of environmental heterogeneity, at both small and large scales, create complex landscapes of selection, which may challenge adaptation, particularly when gene flow is high. One key to multidimensional adaptation may reside in the heterogeneity of recombination along the genome. Structural variants, like chromosomal inversions, reduce recombination, increasing linkage disequilibrium among loci at a potentially massive scale. In this study, we examined how chromosomal inversions shape genetic variation across a species range and ask how their contribution to adaptation in the face of gene flow varies across geographic scales. We sampled the seaweed fly Coelopa frigida along a bioclimatic gradient stretching across 10° of latitude, a salinity gradient, and a range of heterogeneous, patchy habitats. We generated a chromosome-level genome assembly to analyze 1,446 low-coverage whole genomes collected along those gradients. We found several large nonrecombining genomic regions, including putative inversions. In contrast to the collinear regions, inversions and low-recombining regions differentiated populations more strongly, either along an ecogeographic cline or at a fine-grained scale. These genomic regions were associated with environmental factors and adaptive phenotypes, albeit with contrasting patterns. Altogether, our results highlight the importance of recombination in shaping adaptation to environmental heterogeneity at local and large scales.     

A high-density genetic recombination map of sequence-tagged sites for sorghum, as a framework for comparative structural and evolutionary genomics of tropical grains and grasses

We report a genetic recombination map for Sorghum of 2512 loci spaced at average 0.4 cM ( approximately 300 kb) intervals based on 2050 RFLP probes, including 865 heterologous probes that foster comparative genomics of Saccharum (sugarcane), Zea (maize), Oryza (rice), Pennisetum (millet, buffelgrass), the Triticeae (wheat, barley, oat, rye), and Arabidopsis. Mapped loci identify 61.5% of the recombination events in this progeny set and reveal strong positive crossover interference acting across intervals of 相似文献